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Yorodumi- PDB-3fjw: Crystal Structure Analysis of Fungal Versatile Peroxidase from Pl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fjw | |||||||||
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Title | Crystal Structure Analysis of Fungal Versatile Peroxidase from Pleurotus eryngii | |||||||||
Components | Versatile peroxidase VPL2 | |||||||||
Keywords | OXIDOREDUCTASE / CLASS II (FUNGAL) PEROXIDASES / protoporphyrin IX / glycoprotein ELECTRON TRANSFER / LIGNIN PEROXIDASE / LIGNIN DEGRADATION / MANGANESE PEROXIDASE / MN-INDEPENDENT OXIDATION PHENOLIC NON-PHENOLIC AROMATICS / MNII OXIDATION / PEROXIDASE / POLYVALENT PEROXIDASE / Heme / glycoprotein / Hydrogen peroxide / Iron / Manganese / Metal-binding / Secreted / Zymogen | |||||||||
Function / homology | Function and homology information versatile peroxidase / reactive-black-5:hydrogen-peroxide oxidoreductase activity / manganese peroxidase activity / lignin catabolic process / response to reactive oxygen species / hydrogen peroxide catabolic process / cellular response to oxidative stress / heme binding / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Pleurotus eryngii (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Piontek, K. / Martinez, A.T. / Choinowski, T. / Plattner, D.A. | |||||||||
Citation | Journal: To be Published Title: Structural and Site-directed Mutagenesis Study of Versatile Peroxidase Oxidizing both Mn(II) and Aromatic Substrates Authors: Piontek, K. / Choinowski, T. / Perez-Boada, M. / Ruiz-Duenas, F.J. / Martinez, M.J. / Plattner, D.A. / Martinez, A.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fjw.cif.gz | 151.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fjw.ent.gz | 118.5 KB | Display | PDB format |
PDBx/mmJSON format | 3fjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fjw_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 3fjw_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 3fjw_validation.xml.gz | 32.6 KB | Display | |
Data in CIF | 3fjw_validation.cif.gz | 46.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/3fjw ftp://data.pdbj.org/pub/pdb/validation_reports/fj/3fjw | HTTPS FTP |
-Related structure data
Related structure data | 3fkgC 3fm1C 3fm4C 3fm6C 3fmuC 1qpaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34605.699 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pleurotus eryngii (fungus) / Strain: IJFM A169 / References: UniProt: O94753, versatile peroxidase |
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-Sugars , 3 types, 10 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | #7: Sugar | ChemComp-MAN / |
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-Non-polymers , 4 types, 460 molecules
#3: Chemical | #4: Chemical | ChemComp-CA / #5: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 8.0mg/ml protein in 10mM Na-citrate pH 4.0, 1.9M ammonium sulphate, 6% PEG 400, 100mM HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8499 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 14, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8499 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. all: 20657 / Num. obs: 19316 / % possible obs: 93.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.112 / Net I/σ(I): 11.3 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QPA Resolution: 2.8→39.17 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.863 / SU B: 5.741 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.013 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→39.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.993 Å / Total num. of bins used: 8
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